As the key of security authentication, physical layer authentication can save the authentication resources of the upper layer to play an important role in improving the utilization of limited resources. In view of solving the problem of low security in the process of physical layer authentication, a physical layer authentication method based on weightedtype fractional Fourier transform and rotation angle of constellation is proposed. With the low interception of WFRFT, weighted fractional Fourier transform physical layer authentication system based on rotation angle of constellation can reduce the recognition probability of authentication signal by increasing the computational complexity without affecting the signal transmission process. The simulation results show that the recognition probability of the signal outputted through the CRWFRFT system can be infinitely close to 0, and the BER can be close to the theoretical value of the original QPSK. The physical layer authentication security of CRWFRFT system is greatly improved, and further the effective transmission of information is ensured.